Number of observations in the primary dataset at each administrative level by country. Countries with >10 observations displayed as 10.
Number of observations in the primary dataset within different time periods. Year represents the year sampling was completed. Excludes 9 observations missing a study end date.
Number of observations with each study characteristic.
| variable | value | Total | Percent |
|---|---|---|---|
| Study design | Diagnostic test accuracy | 28 | 21.2 |
| Study design | Other | 1 | 0.8 |
| Study design | Surveillance | 93 | 70.5 |
| Study design | Vaccine effectiveness | 10 | 7.6 |
| Sampling quality | High | 37 | 28.0 |
| Sampling quality | Low | 95 | 72.0 |
| Prop lab tested | 0-5 | 12 | 9.1 |
| Prop lab tested | 5-50 | 32 | 24.2 |
| Prop lab tested | 50-95 | 27 | 20.5 |
| Prop lab tested | 95+ | 30 | 22.7 |
| Prop lab tested | Not reported | 31 | 23.5 |
| Num tests | 1 | 106 | 80.3 |
| Num tests | 2 | 19 | 14.4 |
| Num tests | 3+ | 7 | 5.3 |
| N | 1-9 | 1 | 0.8 |
| N | 10-99 | 37 | 28.0 |
| N | 100-999 | 55 | 41.7 |
| N | 1000+ | 39 | 29.5 |
| variable | value | Total | Percent |
|---|---|---|---|
| Prop vaccinated | No | 127 | 96.2 |
| Prop vaccinated | Yes | 5 | 3.8 |
| Prop severe dehyd | No | 121 | 91.7 |
| Prop severe dehyd | Yes | 11 | 8.3 |
| Prop mod dehyd | No | 123 | 93.2 |
| Prop mod dehyd | Yes | 9 | 6.8 |
| Prop female | No | 104 | 78.8 |
| Prop female | Yes | 28 | 21.2 |
| Prop antibiotics | No | 122 | 92.4 |
| Prop antibiotics | Yes | 10 | 7.6 |
| Prop 5 and severe dehyd | No | 126 | 95.5 |
| Prop 5 and severe dehyd | Yes | 6 | 4.5 |
| Prop 5 and dehyd and antibiotics | No | 131 | 99.2 |
| Prop 5 and dehyd and antibiotics | Yes | 1 | 0.8 |
| Prop 5 | No | 100 | 75.8 |
| Prop 5 | Yes | 32 | 24.2 |
| Prop 15 | No | 114 | 86.4 |
| Prop 15 | Yes | 18 | 13.6 |
Proportion of suspected cholera cases that were confirmed positive by A) diagnostic test type, B) quality of sampling methods, where “high” includes all suspected cases or a random or stratified sample and “low” includes convenience or unreported sampling methods, C) age minimum in suspected case definition, where “0” indicates that no minimum age was set, and D) whether surveillance was initiated in response to an outbreak or whether it was routine surveillance or non-outbreak. Each point is an observation. Boxes represent the mean and interquartile range of positivity for each group. Lines extend from the top and bottom of box to the largest positivity value no further than 1.5 * IQR from the box.
Relationship between reported V. cholerae positivity and A) proportion of suspected cholera cases tests that were under 5 years of age, B) suspected cholera incidence rate per 10,000 at study site, C) proportion of suspected cases severely dehydrated, and D) proportion of suspected cases on antibiotics prior to testing. Size of the points is proportional to the number of cases tested, and shapes indicate which diagnostic test was used to confirm V. cholerae infection. Confidence intervals for Spearman rank correlation coefficients estimated using bootstrapping (nrep=1000). Smoothing method is loess (without weights). In B) estimated suspected cholera incidence rates for 2010-2016 (Lessler et al., 2018) were aggregated to the administrative division that best represented each study’s catchment area by dividing the total estimated cholera cases in each area by its estimated population.
Estimate is median sensitivity and specificity pooled across four studies that reported results for all diagnostics tests, as described in Methods. Parentheses show 95% Credible Interval.
| Measure | Test | Estimate (%) |
|---|---|---|
| Sensitivity | Culture | 82 ( 37.5 - 98.7 ) |
| Sensitivity | PCR | 85.1 ( 53.6 - 98.9 ) |
| Sensitivity | RDT | 90.4 ( 55.2 - 99.5 ) |
| Specificity | Culture | 94.3 ( 81.5 - 99.6 ) |
| Specificity | PCR | 94.2 ( 81.1 - 99.7 ) |
| Specificity | RDT | 88.9 ( 54.8 - 99.4 ) |
Posterior distributions of V. cholerae positivity estimated using the random-effects model corresponding to results in Table S4. A) Unadjusted. B) Adjusted for test performance. C) Adjusted for test performance, sensitivity analysis shifting prior on alpha from Normal(0,2) as in A-B to Normal(0.9,2). On the left, prior (green) and posterior distribution (purple) of the global intercept are shown in logit space. On the right, histograms of estimated V. cholerae positivity.
“Unadjusted” is mean V. cholerae positivity (95% credible interval) from random effects meta-analysis without adjustments for test performance. “Adjusted” refers to V. cholerae estimates additionally adjusted for test performance, where the primary analysis includes a Normal(0,2) prior on the global intercept and a sensitivity analysis includes the prior shifted to Normal(0.9,2). “Stratified estimate for high quality…” corresponds to post-stratified estimates of V. cholerae positivity for studies that use high quality sampling methods and whether an age minimum was set in the suspected case definition, as well as whether surveillance was initiated in response to an outbreak.
| Version | Positivity (%) |
|---|---|
| Unadjusted | 46.4 ( 7.7 - 89.2 ) |
| Adjusted for test performance | 52.2 ( 24.2 - 79.8 ) |
| Adjusted for test performance, prior on alpha shifted | 54.8 ( 21 - 85.3 ) |
| Stratified estimate for high quality sample with no known age restriction | 45.9 ( 18.8 - 75.5 ) |
| Stratified estimate for high quality sample with any age restriction | 68.2 ( 32.6 - 97.6 ) |
| Stratified estimate for high quality sample during non-outbreak surveillance | 41.7 ( 11.9 - 77 ) |
| Stratified estimate for high quality sample during outbreak surveillance | 78.2 ( 39.7 - 99.1 ) |
A) Posterior distributions of pooled percent sensitivity and specificity of culture (top), PCR (middle), and RDT (bottom) for detecting V. cholerae O1O139 infections in suspected cholera cases. Dashed lines represent mean values of each distribution. B) “Unadjusted” is mean V. cholerae positivity (95% credible interval) from random effects meta-analysis without adjustments for test performance. “Adjusted for test performance” is estimated mean V. cholerae positivity (95% credible interval), adjusted for sensitivity/specificity of the tests. High-quality stratified estimates corresponds to post-stratified estimates of V. cholerae positivity for studies that use high quality sampling methods and whether an age minimum was set in the suspected case definition, as well as whether surveillance was initiated in response to an outbreak.
Black points indicate mean study-level underlying positivity and 95% Credible Interval (CI). Teal, orange, and purple points indicate the proportion positive reported by study for culture, PCR, and RDT, respectively, and corresponding error bars indicate 95% confidence interval for a binomial probability, estimated with the normal approximation. Studies are labeled by country ISO3 code, whether they used high quality sampling methods, and whether a minimum age was set in the suspected cholera case definition. Studies are split into outbreak and non-outbreak for ease of interpretation.
## I2: 99.99675, 99.99681, 99.99687, ; tau2: 0.9419, 0.96145, 0.97747,
Odds that a suspected cholera case seeking testing or care has a true V. cholerae O1/O139 infection with low sampling quality compared to high sampling quality, with any minimum age set in suspected case definition, and with surveillance initiated in response to an outbreak compared to non-outbreak surveillance (i.e., routine or post-vaccination surveillance).
| Variable | Odds ratio |
|---|---|
| Low sampling quality | 3.8 ( 0.95 - 9.86 ) |
| Minimum age in case definition | 2.33 ( 0.54 - 6.4 ) |
| Outbreak surveillance | 5.71 ( 1.53 - 15.43 ) |